I don't see any direct correlation between the visual design of the site and the command line.
I think the site designers have done a good job within the brand family of both keeping the interface clean and uncluttered, while differentiating it sufficiently from the other Stack Exchange sites.
With the implementation of recent community requested changes, I feel the overall design of the site is about right.
That's not to say that there is no room for improvement, incremental or otherwise. A site's design should evolve and your question is perfectly valid.
So don't be discouraged from participating here by the downvotes. It seems that your call for a complete redesign, however, meant that rather than answer, most of us just indicated a contra view with a downvote.
As to your point about not needing to use the command line in modern distros, that may be technically true; many people do manage to use *nix distros without opening a terminal. But that is like buying an ice cream and just eating the cone—for *nix enthusiasts, the good stuff is on the inside.